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First Insights into the Draft Genome of Clostridium colicanis DSM 13634, Isolated from Canine Feces Anja Poehlein,a Tobias Schilling,b Udhaya Bhaskar Sathya Narayanan,b Rolf Daniela Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germanya; Members of the Applied Bioinformatics in Microbiology Course of the Microbiology and Biochemistry MSc/PhD program, Georg-August University, Göttingen, Germanyb
Clostridium colicanis DSM 13634 is a strictly anaerobic, rod-shaped, and spore-forming bacterium. It produces acids from common sugars such as glucose and fructose. The draft genome consists of one chromosome (2.6 Mbp) and contains 2,159 predicted protein-encoding genes. Received 24 March 2016 Accepted 29 March 2016 Published 19 May 2016 Citation Poehlein A, Schilling T, Bhaskar Sathya Narayanan U, Daniel R. 2016. First insights into the draft genome of Clostridium colicanis DSM 13634, isolated from canine feces. Genome Announc 4(3):e00385-16. doi:10.1128/genomeA.00385-16. Copyright © 2016 Poehlein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Rolf Daniel, [email protected].
C
lostridium colicanis is an anaerobic, rod-shaped, and sporeforming bacterium (1). C. colicanis was isolated from the feces of a male Labrador dog (1). A comparative 16S rRNA gene analysis showed that the bacterium forms a distinct subgroup within the Clostridium rRNA group I. C. absonum, C. baratii, and Eubacterium multiforme were the phylogenetically closest relatives of C. colicanis. These organisms are also typically found in fecal samples (1–3). Chromosomal DNA of C. colicanis DSM 13634 was isolated using the MasterPure complete DNA purification kit (Epicentre, Madison, WI, USA). From the extracted DNA, Illumina shotgun paired-end sequencing libraries were generated, and sequencing was performed with a MiSeq instrument and a MiSeq reagent kit version 3, as recommended by the manufacturer (Illumina, San Diego, CA, USA). Quality filtering using Trimmomatic version 0.32 (4) resulted in 2,106,860 paired-end reads. The assembly was performed with the SPAdes genome assembler software version 3.6.2 (5). The assembly resulted in 83 contigs (⬎500 bp) and an average coverage of 164-fold. The assembly was validated and the read coverage determined with QualiMap version 2.1 (6). The draft genome of C. colicanis DSM 13634 comprises a single chromosome (2.6 Mbp) with an overall GC content of 31.18%. Automatic gene prediction and identification of rRNA and tRNA genes was performed using the software tool Prokka (7). The draft genome contained 14 rRNA genes, 119 tRNA genes, 2,159 proteinencoding genes with function prediction, and 494 genes coding for hypothetical proteins. Interestingly, two CRISPR repeats followed by downstream CRISPR/Cas cluster regions were found. However, putative prophage regions were not detected in the draft genome sequence. C. colicanis DSM 13634 can utilize a large number of substrates (1). It produces several different acids from cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, ribose, and sucrose (1). The formed acids could comprise lactate, acetate, and formate. Correspondingly, putative genes coding for lactate dehydrogenase, phosphotransacetylase, acetate kinase, and formate acetyltransferase were present in the genome of C. colicanis. More-
May/June 2016 Volume 4 Issue 3 e00385-16
over, mannitol and sorbitol are utilized, but only nonacidic metabolic end-products are formed (1). Genes encoding phosphotransferase systems for the substrates glucose, cellobiose, mannitol, mannose, sorbitol, and fructose were found in the genome. Additionally, genes coding for a galactitol phosphotransferase system were present. As described by Greetham et al. (1), nitrate is reduced to nitrite by C. colicanis. We found genes encoding nitrite reductases NasAB (nitrate to nitrite) and NirA (nitrite to ammonia). Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LTBB00000000. The version described here is the first version, LTBB01000000. ACKNOWLEDGMENTS We thank Kathleen Gollnow for technical support. This work was supported by the “Nds. Ministerium für Wissenschaft und Kultur (MWK)” of Lower Saxony (Germany).
FUNDING INFORMATION This work, including the efforts of Anja Poehlein, Tobias Schilling, Udhaya Bhaskar Sathya Narayanan, and Rolf Daniel, was funded by Nds. Ministerium für Wissenschaft und Kultur (MWK). The funders (MWK) had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
REFERENCES 1. Greetham HL, Gibson GR, Giffard C, Hippe H, Merkhoffer B, Steiner U, Falsen E, Collins MD. 2003. Clostridium colicanis sp. nov., from canine faeces. Int J Syst Evol Microbiol 53:259 –262. http://dx.doi.org/10.1099/ ijs.0.02260-0. 2. Hayase M, Mitsui N, Tamai K, Nakamura S, Nishida S. 1974. Isolation of Clostridium absonum and its cultural and biochemical properties. Infect Immun 9:15–19. 3. Suen JC, Hatheway CL, Steigerwalt AG, Brenner DJ. 1988. Genetic confirmation of identities of neurotoxigenic Clostridium baratii and Clostridium butyricum implicated as agents of infant botulism. J Clin Microbiol 26:2191–2192. 4. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for
Genome Announcements
genomea.asm.org 1
Poehlein et al.
Illumina sequence data. Bioinformatics 30:2114 –2120. http://dx.doi.org/ 10.1093/bioinformatics/btu170. 5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.
2 genomea.asm.org
6. García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. 2012. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28:2678 –2679. http://dx.doi.org/10.1093/bioinformatics/bts503. 7. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068 –2069. http://dx.doi.org/10.1093/bioinformatics/ btu153.
Genome Announcements
May/June 2016 Volume 4 Issue 3 e00385-16
First Insights into the Draft Genome of Clostridium colicanis DSM 13634, Isolated from Canine Feces Anja Poehlein,a Tobias Schilling,b Udhaya Bhaskar Sathya Narayanan,b Rolf Daniela Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University, Göttingen, Germanya; Members of the Applied Bioinformatics in Microbiology Course of the Microbiology and Biochemistry MSc/PhD program, Georg-August University, Göttingen, Germanyb
Clostridium colicanis DSM 13634 is a strictly anaerobic, rod-shaped, and spore-forming bacterium. It produces acids from common sugars such as glucose and fructose. The draft genome consists of one chromosome (2.6 Mbp) and contains 2,159 predicted protein-encoding genes. Received 24 March 2016 Accepted 29 March 2016 Published 19 May 2016 Citation Poehlein A, Schilling T, Bhaskar Sathya Narayanan U, Daniel R. 2016. First insights into the draft genome of Clostridium colicanis DSM 13634, isolated from canine feces. Genome Announc 4(3):e00385-16. doi:10.1128/genomeA.00385-16. Copyright © 2016 Poehlein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Rolf Daniel, [email protected].
C
lostridium colicanis is an anaerobic, rod-shaped, and sporeforming bacterium (1). C. colicanis was isolated from the feces of a male Labrador dog (1). A comparative 16S rRNA gene analysis showed that the bacterium forms a distinct subgroup within the Clostridium rRNA group I. C. absonum, C. baratii, and Eubacterium multiforme were the phylogenetically closest relatives of C. colicanis. These organisms are also typically found in fecal samples (1–3). Chromosomal DNA of C. colicanis DSM 13634 was isolated using the MasterPure complete DNA purification kit (Epicentre, Madison, WI, USA). From the extracted DNA, Illumina shotgun paired-end sequencing libraries were generated, and sequencing was performed with a MiSeq instrument and a MiSeq reagent kit version 3, as recommended by the manufacturer (Illumina, San Diego, CA, USA). Quality filtering using Trimmomatic version 0.32 (4) resulted in 2,106,860 paired-end reads. The assembly was performed with the SPAdes genome assembler software version 3.6.2 (5). The assembly resulted in 83 contigs (⬎500 bp) and an average coverage of 164-fold. The assembly was validated and the read coverage determined with QualiMap version 2.1 (6). The draft genome of C. colicanis DSM 13634 comprises a single chromosome (2.6 Mbp) with an overall GC content of 31.18%. Automatic gene prediction and identification of rRNA and tRNA genes was performed using the software tool Prokka (7). The draft genome contained 14 rRNA genes, 119 tRNA genes, 2,159 proteinencoding genes with function prediction, and 494 genes coding for hypothetical proteins. Interestingly, two CRISPR repeats followed by downstream CRISPR/Cas cluster regions were found. However, putative prophage regions were not detected in the draft genome sequence. C. colicanis DSM 13634 can utilize a large number of substrates (1). It produces several different acids from cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, ribose, and sucrose (1). The formed acids could comprise lactate, acetate, and formate. Correspondingly, putative genes coding for lactate dehydrogenase, phosphotransacetylase, acetate kinase, and formate acetyltransferase were present in the genome of C. colicanis. More-
May/June 2016 Volume 4 Issue 3 e00385-16
over, mannitol and sorbitol are utilized, but only nonacidic metabolic end-products are formed (1). Genes encoding phosphotransferase systems for the substrates glucose, cellobiose, mannitol, mannose, sorbitol, and fructose were found in the genome. Additionally, genes coding for a galactitol phosphotransferase system were present. As described by Greetham et al. (1), nitrate is reduced to nitrite by C. colicanis. We found genes encoding nitrite reductases NasAB (nitrate to nitrite) and NirA (nitrite to ammonia). Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LTBB00000000. The version described here is the first version, LTBB01000000. ACKNOWLEDGMENTS We thank Kathleen Gollnow for technical support. This work was supported by the “Nds. Ministerium für Wissenschaft und Kultur (MWK)” of Lower Saxony (Germany).
FUNDING INFORMATION This work, including the efforts of Anja Poehlein, Tobias Schilling, Udhaya Bhaskar Sathya Narayanan, and Rolf Daniel, was funded by Nds. Ministerium für Wissenschaft und Kultur (MWK). The funders (MWK) had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
REFERENCES 1. Greetham HL, Gibson GR, Giffard C, Hippe H, Merkhoffer B, Steiner U, Falsen E, Collins MD. 2003. Clostridium colicanis sp. nov., from canine faeces. Int J Syst Evol Microbiol 53:259 –262. http://dx.doi.org/10.1099/ ijs.0.02260-0. 2. Hayase M, Mitsui N, Tamai K, Nakamura S, Nishida S. 1974. Isolation of Clostridium absonum and its cultural and biochemical properties. Infect Immun 9:15–19. 3. Suen JC, Hatheway CL, Steigerwalt AG, Brenner DJ. 1988. Genetic confirmation of identities of neurotoxigenic Clostridium baratii and Clostridium butyricum implicated as agents of infant botulism. J Clin Microbiol 26:2191–2192. 4. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for
Genome Announcements
genomea.asm.org 1
Poehlein et al.
Illumina sequence data. Bioinformatics 30:2114 –2120. http://dx.doi.org/ 10.1093/bioinformatics/btu170. 5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455– 477. http://dx.doi.org/10.1089/cmb.2012.0021.
2 genomea.asm.org
6. García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. 2012. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28:2678 –2679. http://dx.doi.org/10.1093/bioinformatics/bts503. 7. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068 –2069. http://dx.doi.org/10.1093/bioinformatics/ btu153.
Genome Announcements
May/June 2016 Volume 4 Issue 3 e00385-16
